As far as I understood you want to maintain some level of persistence between your scenes. The thing is, when you load a PackedScene from the file system, e.g.
get_tree().change_scene("path/to/scene.tscn") Godot will load the scene as saved in this file, resetting any changes made during the playthrough.
One way you can achieve what you want is to repack the scene and either keep it in memory and switch to it during the play session, but you will lose the changes when you close the game, or you can save it on disk and load it from there. You can save it in the
const SAVED_SCENE_PATH = "user://path/to/saved_scene.tscn"
const DEFAULT_SCENE_PATH = "res://path/to/scene.tscn"